Related Experiment Video
Updated: Dec 20, 2025
11:19
Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
Published on: November 17, 2019
16.8K
PINE: An Automation Tool to Extract and Visualize Protein-Centric Functional Networks
Niveda Sundararaman1, James Go1, Aaron E Robinson1
1Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States.
Summary
We developed Protein Interaction Network Extractor (PINE), a user-friendly tool for visualizing and exploring proteome and post-translational modification networks. PINE aids in generating novel hypotheses for understanding disease mechanisms.
Area of Science:
- Bioinformatics
- Proteomics
- Systems Biology
Background:
- Mass spectrometry-based proteomics generates large datasets requiring efficient data processing.
- Existing tools for protein-protein interaction (PPI) data are often stand-alone and lack comprehensive network visualization.
- Understanding global proteome and post-translational modification (PTM) networks is crucial for disease mechanism research.
Purpose of the Study:
- To develop an automated, user-friendly graphical user interface application for visualizing and exploring proteome-wide and PTM-based networks.
- To integrate differential expression and PTM site data into network visualizations for deeper biological insights.
- To facilitate hypothesis generation for understanding disease mechanisms through network analysis.
Main Methods:
- Developed Protein Interaction Network Extractor (PINE), a GUI application.
- Implemented automated protein identifier mapping for accuracy.
- Integrated data from multiple public PPI databases.
- Supported overlay of differential expression, statistical significance, and PTM sites on networks.
- Applied PINE to analyze proteome and PTM networks in nonalcoholic steatohepatitis (NASH) mouse models.
Main Results:
- PINE successfully visualizes global proteome and PTM-based networks.
- The tool integrates diverse data types, including differential expression and PTM sites, for comprehensive analysis.
- Case studies in NASH mouse models demonstrate PINE's utility in exploring context-specific regulatory mechanisms.
- PINE effectively assimilates complex networks into functionally enriched pathways and ontology terms.
Conclusions:
- PINE is a powerful, automated tool for visualizing and exploring complex proteomic and PTM networks.
- The application enhances understanding of proteome-wide regulatory mechanisms and PTM-mediated networks.
- PINE serves as a valuable resource for novel hypothesis generation in disease research.
Related Concept Videos
02:26Protein Networks
4.4K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.4K
02:26Protein Networks
2.7K
2.7K
02:04Protein-protein Interfaces
14.4K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.4K
01:57Protein Complexes with Interchangeable Parts
2.8K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
2.8K
01:57Protein Complexes with Interchangeable Parts
2.1K
2.1K